But there is a need to define "minor" if we're going down the path of controlling which populations are allowed to intermix based on their degree of genetic similarity.
If you're saying that nations can do whatever they want within their own borders, you're making the implicit assumption that genetic differences within nations are "minor." If geographical proximity is the main indicator of genetic commonality then this assumption is false: the French region of Alsace has more in common with the Rhineland than it does with Acquitaine, which has more in common with Spain.
The second issue is that you don't seem to mind the dilution of local populations that have different genetics from the mainstream and each other. Yet the fact that these differences are only minor is entirely your idea; to any xenophobes living in some tiny hamlet, you're a chauvinistic authoritarian who supports a political project designed to dilute their culture.
Whether you know it or not, you've crafted a definition of "minor" specifically to include or exclude people according to your personal tastes.